Gene detail

Detailed information of OS493_032536-T1 in Lophelia pertusa

Genomic Location: scaffold_244:55507...62033
NR annotation: KAJ7370361.1, VPS10 domain-containing receptor SorCS1 [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q98930	Sortilin-related receptor (Fragment) OS=Gallus gallus OX=9031 GN=SORL1 PE=2 SV=1
Q95209	Sortilin-related receptor OS=Oryctolagus cuniculus OX=9986 GN=SORL1 PE=1 SV=1
Q92673	Sortilin-related receptor OS=Homo sapiens OX=9606 GN=SORL1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000636 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF15902 all species →	Sortilin-Vps10	Sortilin, neurotensin receptor 3,	Repeat	Interproscan
PF15901 all species →	Sortilin_C	Sortilin, neurotensin receptor 3, C-terminal	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR031778 all species →	Domain	Sortilin, N-terminal	Interproscan
IPR006581 all species →	Domain	VPS10	Interproscan
IPR031777 all species →	Domain	Sortilin, C-terminal	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR050310 all species →	Family	VPS10-related sortilin family receptors	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12106 all species →	SORTILIN RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005794 all species →	Cellular Component	Golgi apparatus	Interproscan
GO:0006892 all species →	Biological Process	post-Golgi vesicle-mediated transport	Interproscan
GO:0016021 all species →	Cellular Component	membrane	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

No KEGG orthology assignment for OS493_032536-T1.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_032536-T1 across 110 RNA-seq samples of Lophelia pertusa. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

110Samples

109TPM > 0

7Conditions

76.2Max TPM

23.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	15.42	24.77
polyp at pH7 6	18	17	13.27	26.64
coral polyp · control treatment	16	16	32.64	63.58
coral polyp · oil and dispersant treatment	16	16	42.80	76.18
coral polyp · oil treatment	16	16	26.39	45.82
coral polyp · dispersant treatment	16	16	22.79	35.83
Polyp	10	10	9.27	20.02

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.77
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.17
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.65
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.61
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.39
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.30
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.82
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.58
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.62
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.10
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.80
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.41
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.00
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.91
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.66
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.46
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.13
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.16
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.64
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.29
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.19
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.62
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.50
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.59
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.06
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.03
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.21
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.33
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.72
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.23
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.07
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.18
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.82
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.14
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.31
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.58
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.16
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.03
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.80
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.19
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.03
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.10
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.77
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.26
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.00
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.83
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.35
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.45
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.28
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.85
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.51
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	76.18
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	68.92
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	67.25
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	64.04
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.30
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.15
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.01
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.52
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.32
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.32
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.54
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.15
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.25
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.72
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.04
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.13
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.82
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.81
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.26
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.74
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.81
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.38
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.69
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.03
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.25
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.30
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.27
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.96
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.48
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.41
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.55
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.50
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.83
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.21
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.02
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.27
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.24
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.33
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.45
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.33
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.82
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.06
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.85
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.58
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.37
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.14
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.81
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.29
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	20.02
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	13.15
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	11.73
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	11.06
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	9.19
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	7.85
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	6.53
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	5.98
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	4.76
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.41

Source: CnidoSite RNA-seq expression matrices (LPERT_TPM, StringTie quantification over 110 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.